The goal of this research is to determine the regulatory circuits in S. cerevisiae that control filamentation, a key morphogenetic even in pathogenic and non-pathogenic fungi. Our deletion library in the S. cerevisiae Sigma strain, when compared with the reference library in S288c, enables a comprehensive assessment of the genetic mechanisms leading to different filamentation and viability phenotypes for the same mutation in two different laboratory strains. This problem is the same one confronting human geneticists tackling the heritability of complex disease traits. The analysis of the filamentation/adhesion trait, which is important for the ability of fungi to adhere to medical devices, revealed that a m6A modification of mRNA, catalyzed by the IME4 gene, is a key post-trancriptional event that controls the decision to enter the filamentation or meiotic pathway. Experiments will determine the function of this m6A modification and whether the disappearance of the mark is due to demethylation or specific messenger degradation. The signal transduction pathway (the filamentation MAPK pathway, fMAPK) that activates filamentation genes in one strain (Sigma) is not required in the other (S288c), which has evolved polymorphisms that bypass the necessity for this pathway. The analysis of this alternative filamentation pathway will reveal the underlying network within which these polymorphisms develop. Of particular importance are two cis-acting non-coding RNAs, PWR1 and ICR1, that have been shown in Sigma to be a cis-acting toggle controlling the expression of the adjacent FLO11 gene, which is required for filamentation. Experiments are designed to determine whether these non-coding RNAs are involved in FLO11 expression in S288c, where a different set of trans- acting factors activate FLO11. These experiments will shed new light on the ubiquity of ncRNA regulation within a species. Our genome-wide comparison also identified conditionally essential genes, genes whose function is required for viability in one strain but not the other. The analysis of the genetic differences that lead to suppression of lethality has raised the possibility that extra-chromosomal elements (mitochondrial DNA) and dsRNA interact with chromosomal polymorphisms to cause variation. The discovery of these nucleo/cytoplasmic interactions adds an unanticipated dimension to the analysis of complex traits.